Scroll to navigation

GMT-MUSIC-PATH-SCAN(1p) User Contributed Perl Documentation GMT-MUSIC-PATH-SCAN(1p)

gmt music path-scan


gmt music path-scan - Find significantly mutated pathways in a cohort given a list of somatic mutations.


This document describes gmt music path-scan version 0.04 (2018-07-05 at 09:17:13)


gmt music path-scan --gene-covg-dir=? --bam-list=? --pathway-file=? --maf-file=? --output-file=? [--bmr=?] [--genes-to-ignore=?] [--min-mut-genes-per-path=?] [--skip-non-coding] [--skip-silent]

 ... music path-scan \
        --bam-list input_dir/bam_file_list \
        --gene-covg-dir output_dir/gene_covgs/ \
        --maf-file input_dir/myMAF.tsv \
        --output-file output_dir/sm_pathways \
        --pathway-file input_dir/pathway_dbs/KEGG.txt \
        --bmr 8.7E-07


Directory containing per-gene coverage files (Created using music bmr calc-covg)
Tab delimited list of BAM files [sample_name, normal_bam, tumor_bam] (See Description)
Tab-delimited file of pathway information (See Description)
List of mutations using TCGA MAF specifications v2.3
Output file that will list the significant pathways and their p-values


bmr Number
Background mutation rate in the targeted regions

Default value '1e-06' if not specified

Comma-delimited list of genes whose mutations should be ignored
Pathways with fewer mutated genes than this, will be ignored

Default value '1' if not specified

Skip non-coding mutations from the provided MAF file

Default value 'true' if not specified

Make skip-non-coding 'false'
Skip silent mutations from the provided MAF file

Default value 'true' if not specified

Make skip-silent 'false'


Only the following four columns in the MAF are used. All other columns may be left blank.

 Col 1: Hugo_Symbol (Need not be HUGO, but must match gene names used in the pathway file)
 Col 2: Entrez_Gene_Id (Matching Entrez ID trump gene name matches between pathway file and MAF)
 Col 9: Variant_Classification
 Col 16: Tumor_Sample_Barcode (Must match the name in sample-list, or contain it as a substring)

The Entrez_Gene_Id can also be left blank (or set to 0), but it is highly recommended, in case genes are named differently in the pathway file and the MAF file.


For example, a line in the pathway-file would look like:

  hsa00061    Fatty acid biosynthesis    Lipid Metabolism    31:ACACA|32:ACACB|27349:MCAT|2194:FASN|54995:OXSM|55301:OLAH

Ensure that the gene names and entrez IDs used match those used in the MAF file. Entrez IDs are not mandatory (use a 0 if Entrez ID unknown). But if a gene name in the MAF does not match any gene name in this file, the entrez IDs are used to find a match (unless it's a 0).


 Michael Wendl, Ph.D.


This module uses reformatted copies of data from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database:

 * KEGG -
2018-07-05 perl v5.26.2